Monday, September 26, 2011

One of my new favorite webcomics is Ninja Nun (http://www.robertahoyt.com/Comic92.html). Click on the crossed rulers below the comic and start from the beginning. No, it's not science based, but I happen to know that artist has a respectable pedigree in science - Robert Anson Hoyt is a published science fiction author, and named for the SF author Robert A. Heinlein (R.A. Hoyt having been born on R.A. Heinlein's birthday). He comes from a family of SF writers and is himself a pre-med student. In fact, he has even been known to refer to himself as a "lab rat"!

If there is any doubt that Robert A. Hoyt has a wicked sense of humor, check out the comics immediately following and preceding the one linked above, then check out this highly appropriate bonus comic (http://www.robertahoyt.com/Bonus3.html). Yes, Robert loves ties. No, we couldn't get him to stop wearing them even in the lab, cleaning rat cages. He'll make a fine surgeon someday with his attention to detail and cutting wit.

So sharpen your ruler, sit back and enjoy the adventures of Sister Agnus Day, the "Ninja Nun."

All I can say is WOW! Wow to the technology. Wow to the science, and Ouch, to the poor subjects who spent 3 hours in the MRI scanners.

To the journalist/publicity department... yeah, not so much.

This is really neat stuff. The scientists at UC Berkeley used magnetic resonance imaging to map brain activity as their subjects viewed a number of video scenes. Most of the readers to this blog probably know that MRI is used to take pictures of the inner structure of the brain and soft tissues of the body. Chemists and physicists may remember that the basis of MRI is nuclear magnetic resonance - in a strong magnetic field, hydrogen bonds orient and spin in the same direction. A radio signal causes them to flip orientation, and the resulting energy release can be detected. Water molecules have plenty of hydrogen bonds, brain and soft tissues have plenty of water, thus MRI is used to map the density of water in the brain. MRI can also work with oxygen, and blood contains both water and oxygen.

Functional MRI (fMRI), as used in this study, goes one step further, it maps changes in brain activity on based on the blood flow to active brain areas. The apparatus is a bit cumbersome, and it's not exactly "real-time" but fMRI can tell a lot about overall brain activity.

What this study shows is that the scientists were able to build a database of brain activity in response to video. Then when an image was shown to the subjects, the computer was able to determine which image was shown to the subjects. Essentially what the experiment did was to reconstruct the brain's code for visual scenes.

This is neat stuff!

Understanding the brain's internal coding scheme is a major accomplishment, and this experiment goes a long way to demonstrating exactly that.

But reading dreams? I'm sorry, but that's way too much of a stretch for this experiment.

(1) The fMRIs were taken as the subjects were viewing various scenes. They were not taking while "imagining" scenes, from recollections, or from dreams.

(2) Vision activates multiple areas of the brain that are not active during imagining or dreaming. The primary visual cortex and input pathways are not active unless the images are actually present to be viewed. On the other hand, the sensory association cortex and memory systems are active during both vision and recollection.

So in short, a reconstruction of dreams or memory is missing half of the data that would be present when the subject is viewing scenes, images and video as in the current experiment.

While extremely important and exciting, the UC Berkeley findings are not mind reading or even dream reading (ala "Brainstorm"). Can the technology tell us a lot more about how the brain encodes information? Yes. Is it mind reading? Well, not exactly, and certainly not in "real-time."

Sunday, September 18, 2011

No, I am not stopping this blog, but I need to adopt an irregular update schedule - in fact, it should be fairly obvious that I already have.

There is an unfortunate truth about blogging... if you do it right, it's a job. The unfortunate part is that it is quite often a second, third or fourth job on top of other duties. I started this blog as a way to talk about Science and provide structure and feedback for writing The Lab Rats' Guide to the Brain. It has been successful. I appreciate the readers and great questions. They have assisted me in writing and refining what I have written for the Guide.

However, I do have a day job. As medical school research-and-teaching faculty, my employer figures that it is a 55-60 hr/week job. That includes time at home working on writing up scientific results and set-up for teaching lectures. Reviewing scientific manuscripts, and grants, and writing my own grant applications is extra. Preparing teaching materials (for those of us with more than 80% research commitment) is extra. Committee work (essential for promotion) is extra. Putting in the additional effort to be promoted... is extra.

So the Day Job is job number one. The ancillary teaching, reviews and extra work that will assist in my promotion and tenure prospects next year is Job 1.5. Family is Job 2, my fiction writing has been Job 3 and I had hoped that the blog would fit in nicely as Job 4.

It hasn't worked that way. I tried an every-other-day schedule and a three-nights-a-week schedule, and this Blog became Job 2, and nearly Job 1.5. I suppose I write too much in each blog, it takes me 1-2 hrs for each Guide post because I am researching details, searching out illustrations (public domain if possible) and comparing results with existing websites. There have been times I could take an hour out of the day job and write part or all of a blog - usually while eating lunch or waiting on a computerized analysis to complete - but those opportunities have become fewer and further apart.

But the most unfortunate truth of blogging is the effect on creativity. I have written before about the fact that I can write science or I can write fiction, but cannot intermingle the two. I have to clear my head of the professional work in order to write the recreational stuff. The Guide has been beneficial, in that it *is* science, and I do not have to completely shift gears from my work in order to write.

But it has nevertheless impaired my writing ability. I have three writing commitments due this fall, and have not been able to work on any of them in three months. I must make time to complete the projects... at a time when I find myself having to do more grant and manuscript writing at work. "Something's gotta give," and I am afraid that it is regular blog posts.

I will still continue to blog. I will post the final sections of the Guide, comment on new and interesting Science, and continue to answer questions.

I appreciate all of my followers and occasional readers, and encourage you to sign up to follow this blog either via Blogger or Facebook (NetworkedBlogs). I will continue to email the blog to Sarah's Diner in Baen's Bar, whatever form that forum eventually takes. Sign up, and you will be notified or emailed the blog when it posts.

Again, I am not discontinuing, just moving to a less regular posting schedule. I will continue blogs at least weekly, and will try to continue Monday Funnies as long as I have material.

Wednesday, September 14, 2011

Before returning to the mailbag posts, I want to take the time to post some links to recent video projects. The flip-side to Teddy's Rat Lab is the TR Productions home page which features photos and videos from various science fiction panels. Some of the earlier work can be found at http://teddroberts.com, complete with downloads in multiple file formats. I tried hard to work out a streaming video service for the website, and need to get some of the more recent videos linked on-site.

All of the more recent work can be found at my YouTube channel: http://www.youtube.com/TeddRoberts once the length and size restrictions were eased. Particular features of the channel include the recent Dragon*Con videos. At the upper left is the "Air Shark" swimming through the lobby of the Atlanta Hyatt Regency. Below left is the flash mob tribute to 2011 Campbell Award nominee, NY Times bestselling author Larry Correia and his Monster Hunter International series.

Several of the videos are short subjects, promotions, teasers, and music ("filk") - some are much longer full panels and skits from various SF conventions. For Music, check out "Monster Hunter Ballad" written and sung by Gray Rinehart (by the way, there's more coming from Gray as soon as I can get the video processed). For pure zombie-hunting fun, watch "Killing the Undead" a pro-writer panel from last year's LibertyCon - but for absolute zaniness, there's "The Making of Ghost: The Movie" in several versions, the YouTube HD release of the Dragon*Con 2008 version, and the download version of the LibertyCon preview skit available on the website.

There are many panels uploaded, and more to come. Keep watching for new releases. Like, subscribe or friend the channel, share the videos, comment, and rate them.

Monday, September 12, 2011

Once upon a time there was a "scientific" journal. Unlike most journals that publish results from experiments that have been repeated and statistically confirmed, the journal specialized in really neat results that `looked real, but couldn't be repeated. Even though founded in 1955 to publish science humor and satire, the Journal of Irreproducable Results had a serious side - being the last resort for publishing results that could not (will never, and probably should never) be replicated.

In 1994, there was a bit of a tiff with the new publishers (who bought out the old publisher), and the editor and most of the staff left to found a new magazine - the Annals of Improbable Research. Like its predecessor, AIR takes a humorous, even satiric look at scientists and science research. It particularly seeks out factual research with a whimsical bent.

PS - Addendum: I did not mean to slight The Journal of Irreproducable Results. BOTH journals provide a slightly serious, mostly fun look at science. The J.I.R. site is: (www.jir.com) and I am certain they would appreciate our patronage!

Friday, September 9, 2011

I haven’t stopped to answer questions based on the Lab Rats’
Guide to the Brain for quite some time.I have received comments in the blog, as well as in the Baen’s Bar
online community.Unfortunately I
haven’t been entirely timely in answering the ones that require more than just
a quick answer – but I do save them for later use.

So for the next several days I will work through the backlog
and answer your questions about the brain.So without further ado…

[squeak]

What’s that, Ratley?

[squeak]

Um, yeah, I suppose I should.

[squeak]

Right.Ratley is
going to gather the other LabRats around for this.Since I still have a scientific conference
and Dragon*Con this week, I’m going to let them tackle the mail while I finish
my two presentations for the meeting.So, I’ll just set up this automatic translator and get back to fixing
slides.

[squeak... er, excuse me.Hi.I'm Ratley, and I'm
supervisor of the LabRats.What Speaker
seems to have forgotten is that it has traditionally been the job of the
LabRats to answer the mail.The fact
that he hasn't let us out of the lab much these past few months is one of the
reasons we've gotten so far behind in reading the mail.We each have our different areas of
expertise, so the LabRats will share the task of answering questions.For the first couple of questions, I'm going
to let Ratso answer.He's pretty smart,
even if he does prefer to spend too much time in the kitchen and talk like ...
well, a rat!]

Ratso:Yo, Ratboy, I
*resemble* dat remark!Okay, on wit' da
program heah:Chris writes:“I’m working on a story where my character
has to get used to his new super abilities.Just how fast does the brain process?If thoughts, movements and reflexes were to be sped up, how hard would
it be for my character to cope and learn how to use them?"

Well, Chris-boy, it's like dis – da brain is only as fast as
its parts.To understan' how fast dat
can be, ya gotta figger out how fast is each link in da chain.Da neurons, well, dey's pretty fast.Takin' the time from the first chemical
activation of a synapse to when da action potential starts is about 2
milliseconds.Action potentials (http://teddysratlab.blogspot.com/2011/02/piece-of-action-potential.html)
travel to the other end of da neuron at about 10 meters per sec.If da neuron is a *long* sensory or motor
control neuron for da body, it has a special insulatin' coating called
"Myelin" dat speeds up da action potential to about 100 meters/sec.
Once da action reaches da end of the neuron, neurotransmitter chemicals are
release to start da process all over again in da next neuron.Da chemical part takes about 2-3
millseconds.

So each link in da chain, dat is, each neuron
"synapse" takes about 5 millseconds, and it takes an action potential
less than 10 milliseconds to travel either from brain to brain area, or from
brain to hands – about 20 milliseconds to get to da feet.Dat's pretty slick, if ya ask me!Multiply dat by about 4 or 5 times for
connections between neurons and parts of brain controlling an action.I like connections.I'm a connections kind of guy myself!

So yeah, da brain can process pretty fast, almost anything
ya wanna do can be completed in about 100 milliseconds.If'n ya wants to write a story wit'
everything speeded up, ya can prob'ly get about 10 times da speed outta just
makin' the chemical and electrical connections more efficient, but like any
good exercise, ya gotta learn ta use it.In fact, it'll be jus' like any new skill: practice, practice, Practice!

***

Ratley: Thank you, Ratso.Perhaps you should get back to the stockroom, there's a fellow named
Guido back there saying something about kitchen supplied that fell off of a
truck?

For the next question, perhaps we should defer to our
resident master of motor skill, Nestor:

Nestor:Why thank you
old chap, that's mighty kind of you.Be
a good lad and hand me that letter then?Ah yes.In response to “The Six
Senses (and maybe more…)” Anonymous asks:“What about the ability to do complex tasks requiring fine motor skill,
with your hands out of sight and in all sorts of odd positions? I do that quite
often when working on cars and other mechanical things. It's like I can
"see" with my hands, often it helps if I close my eyes.”

Dear Sir:

What you are describing is commonly misnamed as "muscle
memory."A skill practiced to a
point where it becomes automatic.The
muscles move the way they are supposed to every time, you don't have to think
about it.

In reality, this should be termed "cerebellar
memory."The cerebellum is the part
of the brain most responsible for coordinating movements.It is quite heavily connected to all those
parts of the brain involved in a movement or reflex.For instance – when moving your arm, you must
move the arm muscles and joints, but you also turn your head, shift your weight
on your feet, twist slightly at the waist and often look at the movement.If you don't look, you'll probably do it ok,
but you may not be quite as accurate in the motion.Now try to move your arm while keeping the
rest of your body completely still!Quite a bit of bother, no?That
is because the brain issues all of those commands, coordinated by the
cerebellum, and when you consciously override the reflexes, the cerebellum
requires all new programming.Sort of
like learning to raise a single eyebrow.

Soldiers and athletes understand the concept very well.Actions must be learned so well that they are
automatic – however it really is the brain learning, and not the muscles.As for your question, it's all the same,
righty-o?Because we have learned
how our muscles move while we watch them, it is right simple to imagine
those movements, then perform them with our eyes closed.You "see" with your hands because
the brain uses all of the information about movement and position and then
calls upon memory to fill in the missing pieces.All of the connections from the cerebellum to
the motor and sensory areas of the brain, plus the connections to visual and
auditory tracking centers in the brainstem provide a "map" of the
body in 3-D space.Quite amazing, if I
may say so myself.

Now, if you will excuse me, my tail seems to be caught in a…
Oh bother!

***

Ratley:Thanks,
Nestor.We'll send the Jaws of Life in
for you, don't worry.

Sandra writes:Dear
Speaker:

My daughter's domesticated pet
rats have been vocalizing a lot lately. The other day I walked into her room
and told her it was time to get up. A rat (in the cage) poked its head out of
its sleeping hammock and said *squeak-squeak*. Later, as the two rats were out
of their cage, playing, they froze when the big black dog stepped into the
room. I sternly told the dog to leave (she's not allowed in that room) and
after the dog left, the biggest rat rushed to my side, staring at the door, and
growled and squeaked. I've never heard her (the rat) make these sounds before,
and it sounded like she was scolding the dog.

I realize we humans tend to
anthropomorphize our pets, but could these rats be trying to communicate? And
what about the personalities these rats seem to have? For many people, rats are
vermin and pests; for cats and dogs they are prey. How can these rats be so
charming?

[squeak!]

Ratley:What's that,
Ratface?Cousins you say?Yes, Indeed.They must be!

Dear Aunt Sandra – (for if the rats are our cousins, you
must be our Aunt!) – domestication of any animal is a learned process.What you are describing represents two
aspects of learning that apply to many animals.If you have ever watched circus animals, movie dogs or the "Walrus,
Otter, Sea Lion" show at Sea World you have seen the results of what is
called "operant conditioning."Most folks should recall reading or learning about Pavlov's experiments
in classical conditioning.Pavlov rang a
bell simultaneous with the smell/taste of food.The dog salivated at the food stimulus, and eventually learned to
salivate at the sound of the bell alone.In behavioral terms, we talk about an "unconditioned stimulus"
(UCS) – that is, a stimulus that produces the desired response without
learning.In the Pavlov example, smell
of food is the UCS and salivation is the response.Then there is the "Conditioned
Stimulus" (CS) – this is a stimulus (bell) that we *want* to produce the
same response as the UCS.So we present
UCS and CS together for a *lot* of repetitions – usually with the CS occurring
before the UCS.Eventually the
conditioned response (salivation) starts to occur after the bell, but before
the smell of food.Once that happens, we
call it a "conditioned response" (CR). Once our experiment begins to
look like this:CS – CR – then UCS, we have
conditioned the animal and can even omit the smell of food (UCS) and still get
salivation (CR) just by ringing the bell (CS).Voila - Pavlov's classic experiment in behavioral conditioning, also
known as "classical conditioning."

Operant conditioning differs in that we actually teach the
animals a chain of UCS stimuli, and those stimuli require the animal to *do*
something.In the Sea World show
example, the sea lion is conditioned to know that ringing a bell means a food
reward will be given.This is classical
conditioning, but then we add a twist – now the sea lion gets a chance to
explore the bell – if it rings the bell itself, it gets a fish!This is the first essential step in operant
training, the animal makes its own response and receives a reward.To make more complex behaviors, we just train
in one preceding step at a time – before the sea lion can ring the bell, it
must climb some steps.So in this step
we have two operant phases: (1) climb steps, in order to be able to (2)
ring bell, to receive the reward.It's
just like training dogs, horses, or even people.Once enough steps are "chained"
together, our sea lion becomes the star act and appears to be behaving just
like a human – but it's only conditioning at work.

Your pet rats have become conditioned.They know which humans feed them, take them
out for exercise, and protect them from predators.This is where the second aspect of learning
comes in: dominance.Normally, dogs are
predators to rats, as are humans.Trust
me.We lab rats know all about
that!However, in caring for our
cousins, and keeping the other predators away (!) we come to recognize you
humans as the dominant creatures in our environment.As long as we remain conditioned to you, and
you protect us, we'll act submissive to you.

Now submission comes in many forms.Speaker tells us stories of working with
primates.If there's one big mean monkey
in a colony, the other monkeys are submissive, and most will not challenge the
"Alpha."However, if the Alpha
attacks a smaller monkey and a human intervenes, the lesser monkeys look
to the human as Alpha (and sometimes even the Alpha will defer to the
human).The human is the more dominant
creature and protector.In animal
behavior terms, that's usually called "mate," but is also
"companion" with the commonly domesticated animals such as dogs and
horses.

So what you are seeing is a bit of
anthropomorphization (hmm, Ratfink must have left that word lying around here)
but also a result of the conditioning and dominance hierarchy among animals.

But then again, it might just be that our cousins are a bit
smarter than you think!

***

Oops, here comes Speaker, time to get back to work.

Speaker:Thanks,
Ratley.My meetings are over, as is
Dragon*Con.There's a few more letters
in the mailbag here, and I'll try to get to those next week.I hope the answers were informative, but you
can never tell with LabRats!

Wednesday, September 7, 2011

Last weekend was Dragon*Con - the largest Science Fiction / Fantasy / Comic / Anime / Gaming / Media convention in the southeastern U.S. For those of my readers not familiar with Dragon*Con, but who may have heard of San Diego's ComicCon, Dragon (or D*C) is a bit smaller... "only" 45,000 in attendance. Whereas ComicCon is essentially a tradeshow, originally about comics and graphic media, it grew to be the premier "trade" show for SF and Fantasy TV shows and movies.

On the other hand - D*C is about fans - yes, there were panels filled with the stars, writers, directors and producers of TV and movies - but there were also tracks for anime, producing animated music videos, costuming, writers, survivalists, dark fantasy, noir detectives, alternate history, SF literature - and yes, science. These tracks gave a chance for interaction between fans, writers and all interested parties. THis is the first of several blogs regarding D*C, but the only one to run exclusively in this blog space, so I will concentrate on giving an overview of the "Science in Science Fiction" nature of the panels I experienced at D*C.

To start with, I participated in panels in the SF Literature, Apocalypse Rising and Science tracks. Panel titles included: "Year 2" (rebuilding civilization after the apocalypse), "Science and Science Fiction" (how science informs the arts and how art informs science), "Global Insurgency" (how wars will be fought - and survived - in the future) and "Zombie Science" (a look at fact and speculative fiction about zombies).

For "Science and Science Fiction, my co-panelists included Stephanie Osborn, Les Johnson, and Chuck Gannon. Steph and Les are real rocket scientists and Chuck is a professor. All three are published Science Fiction writers, so we really did know what we were talking about. The panel subjects discussed how good science fiction relies on believable science (and sometimes on just so-so science) so as not to be fantasy in reality. We discussed how much can be left to the reader, what needs to be explicitly explained, and when the accuracy of science has to make way for good storytelling. One of the most notable outcomes of the panel was the revelation that so much of what we take for granted in modern society - wireless telecommunications (cell phones and satellites), realistic broadcast entertainment (HD TV), weather forecasting (satellites again), transportation, personal computers and even voice-sensitive computers you can carry in your shirt pocket (smartphones) have been inspired by science fiction.

In the Apocalypse Rising panels "Year Two" and "Global Insurgency", SF writer and SurvivalBlog contributing Editor Michael Z. Williamson scared us all into realizing that urban environments are not conducive to survival after the fall of civilization. On the other hand, they'd make great resource areas (if they can be reached and aren't picked clean) for rebuilding civilization. Conversations on these panels included such topics as rebuilding the sciences, what trades and knowledge are essential for survival, how to find information on basic medical care/first aid, and how to prepare for "everyday" emergencies such as storms, floods, fires, and earthquakes.

Finally, in "Zombie Science" we discussed the real science behind zombies. The undead represent fear of the unknown, the psychological uncertainty of "the other," and a pretty good metaphor for disaster preparedness. With 4 scientists and 2 writers, we discussed where the zombie myth comes from, dissed the various fictional settings and sources of zombies (Parasites, Yes! Radiation, No.) and talked about actual biological parallels to the "mindless" behavior that is one definition of zombiehood. We also used biology and physics to come up with the best means of defense and dealing with zombies (thermobaric explosives for the win!).

All-in-all, Dragon*Con is a great place to talk science and science fiction, not to mention engage in some great conversations (such as the one mentioned Monday where regarding things that go Boom! and the fun of model rocketry gone awry!). I'll be writing some more blogs to be posted in other venues, but I'll link them here when they are up. I'll also post links to videos and podcasts of the panels as I get them prepared.

---

Up next - Mailbag posts where I *finally* answer those questions you've mailed in.

Until next time - take care of your brain - after all, the Zombies will if you don't!

Monday, September 5, 2011

Just returned from Dragon*Con. Lots of fun, not a lot of sleep. Today's humor links are not specifically science related, but... I was listening to the panel on webcomics...

For context, I was specifically waiting for Howard Tayler, creator of Schlock Mercenary (which I linked in a previous post), and he was moderating a panel on webcomics. There were two panelists in particular whose work I appreciate - who sometimes include humor that touches on science - and whose humor not only includes some things with which I am familiar, but who will have some Dragon*Con-related content in the near future.

I'll get to those links in a minute. But first:

Howard Tayler is one of those authors who can easily "hold court" in a room of fans and friends irrespective of location. In the car, in the restaurant, in the hospitality suite - Mr. Tayler can sure tell a story. That is why his webcomic, Schlock Mercenary is more than just a daily comic, it is a story told in graphic, serial format. He claims that someone else is the inspiration for his "resident mad scientist" Kevyn Andreason, but considering the tales he told of Boy Scout camp cooking, model rockets gone awry, and miscellaneous things that go boom, it is clear that Howard Tayler retains a bit of that mischievous mad scientist nature himself. I will reiterate that of all of the webcomics I read, Schlock Mercenary remains at the top of those that tickle my funny bone.

And now for those other webcomics: "The Devil's Panties" I admit, I don't always follow it, but when I do, I find it to be a great humorous look at life. Then there's the artist. Spend any time around Jennie Breeden and you can't help but feel her infectious energy and enthusiasm. From the big boots to threatening men in kilts with a leaf-blower, SF conventions without Ms. Breeden in attendance do not know what they are missing. "Kevin and Kell" One of the great mismatched couples of SF and fantasy. Bill Holbrook is acknowledged as one of the most experienced and skillful graphic artists. The link is to his Sunday Dragon*Con tribute strip. I think he captured it pretty well.

Over the next week I will resume regular blogging. Thanks for your understanding, I needed this break to recharge. Up next we have mailbag posts featuring Brain Science questions from readers, a couple of science and science fiction panel reports from Dragon*Con, then we will resume The Lab Rats' Guide to the Brain with topics on "Brain disorders as plot devices."

Thanks for your patience, welcome to new readers. Check out the backlist of blogs at right for content from The Guide and other brain science topics.